By the way, I've never run the code in question.
Does the orientation in the pdb matter? I.e. is the ligand positioned
relative to the protein?
It's another shot in the dark, but what if you rotated the ligand or (if
positioning is relative) the whole complex?
Bill
On 2/22/17 12:45 AM, Mitul Srivastava wrote:
> Dear Ross,
> There are no close contacts. And I have successfully
> completed simulation using this ligand on three complexes. The protein is
> same, ligand is same, but on others it has worked properly but only in this
> case it's showing this error and I am surprised why it's happening. I have
> no clue what to do.
>
> On Wed, Feb 22, 2017 at 2:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> It looks like SQM simply doesn't like those coordinates. Are you sure
>> there aren't any close contacts?
>>
>> Bill
>>
>>
>> On 2/22/17 12:28 AM, Mitul Srivastava wrote:
>>> yes it is, this is the error coming, you can also find in attached.
>>>
>>> QMMM: ERROR!
>>> QMMM: Unable to achieve self-consistency to the tolerances specified
>>>
>>> On Wed, Feb 22, 2017 at 1:57 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>>> Is there an sqm.out file left behind? If so, how does it end?
>>>>
>>>> Bill
>>>>
>>>>
>>>> On 2/22/17 12:24 AM, Mitul Srivastava wrote:
>>>>> "Error: cannot run "/apps/gnu/gcc-4.8.5-4/amber/16/amber16//bin/sqm -O
>>>> -i
>>>>> sqm.in -o sqm.out" of bcc() in charge.c properly, exit"
>>>>>
>>>>> this is the error.
>>>>>
>>>>> And I have not added hydrogens before running antechamber.
>>>>>
>>>>> On Wed, Feb 22, 2017 at 1:39 PM, Goetz, Andreas <agoetz.sdsc.edu>
>> wrote:
>>>>>> You still haven’t told what is the error that you encounter with
>>>>>> lig_new.pdb. And did you add hydrogen atoms before running
>> antechamber?
>>>>>> As a note aside, if you have twice the same ligand, you have to run
>>>>>> antechamber only once.
>>>>>>
>>>>>> All the best,
>>>>>> Andy
>>>>>>
>>>>>> —
>>>>>> Dr. Andreas W. Goetz
>>>>>> Assistant Project Scientist
>>>>>> San Diego Supercomputer Center
>>>>>> Tel: +1-858-822-4771
>>>>>> Email: agoetz.sdsc.edu
>>>>>> Web: www.awgoetz.de
>>>>>>
>>>>>>> On Feb 21, 2017, at 11:52 PM, Mitul Srivastava <mitul.thsti.res.in>
>>>>>> wrote:
>>>>>>> Sir,
>>>>>>> I have two complexes with same ligand only there docking
>>>> position
>>>>>>> is different. When I am running antechamber with 1st attached file
>> from
>>>>>>> where i have extracted the ligand and saved it as "lig.pdb", its
>>>> running
>>>>>>> properly generating every file. But when I am running antechamber for
>>>>>>> second attached file, its not running. Though my deepest query is
>> that
>>>>>> both
>>>>>>> the ligands are same only there is difference in coordinates even
>>>> though
>>>>>>> second is not running.
>>>>>>>
>>>>>>> I think I am clear this time.
>>>>>>>
>>>>>>> Please help me
>>>>>>>
>>>>>>> On Wed, Feb 22, 2017 at 1:12 PM, Goetz, Andreas <agoetz.sdsc.edu>
>>>> wrote:
>>>>>>>> What do you mean with “running fine” and “sqm error”? Without
>> details
>>>>>> it’s
>>>>>>>> hard to help. The pdb files don’t have hydrogen atoms, did you add
>>>> these
>>>>>>>> before running antechamber?
>>>>>>>>
>>>>>>>> All the best,
>>>>>>>> Andy
>>>>>>>>
>>>>>>>> —
>>>>>>>> Dr. Andreas W. Goetz
>>>>>>>> Assistant Project Scientist
>>>>>>>> San Diego Supercomputer Center
>>>>>>>> Tel: +1-858-822-4771
>>>>>>>> Email: agoetz.sdsc.edu
>>>>>>>> Web: www.awgoetz.de
>>>>>>>>
>>>>>>>>> On Feb 21, 2017, at 11:28 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>>>>>>>
>>>>>>>>> Not sure what the SQM error is, but looking at the pdb's, I notice
>>>> the
>>>>>>>>> 2nd has explicit '+'s in it, which might confuse some programs.
>>>>>>>>>
>>>>>>>>> Bill
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 2/21/17 10:53 PM, Mitul Srivastava wrote:
>>>>>>>>>> ---------- Forwarded message ----------
>>>>>>>>>> From: <amber-owner.ambermd.org>
>>>>>>>>>> Date: Wed, Feb 22, 2017 at 12:03 PM
>>>>>>>>>> Subject: SQM Error
>>>>>>>>>> To: mitul.thsti.res.in
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> You are not allowed to post to this mailing list, and your message
>>>> has
>>>>>>>>>> been automatically rejected. If you think that your messages are
>>>>>>>>>> being rejected in error, contact the mailing list owner at
>>>>>>>>>> amber-owner.ambermd.org.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ---------- Forwarded message ----------
>>>>>>>>>> From: Mitul Srivastava <mitul.thsti.res.in>
>>>>>>>>>> To: amber.ambermd.org
>>>>>>>>>> Cc:
>>>>>>>>>> Date: Wed, 22 Feb 2017 12:03:04 +0530
>>>>>>>>>> Subject: SQM Error
>>>>>>>>>> Hello Amber Users,
>>>>>>>>>> i am doing protein-ligand complex
>> study
>>>>>>>> and I
>>>>>>>>>> am facing a very unique error where the error is showing while
>>>> running
>>>>>>>>>> ANTECHAMBER on Amber16. The error is -- I have used two proteins
>>>> with
>>>>>>>> same
>>>>>>>>>> ligand. In attached file "lig.pdb" of one complex is running fine
>>>>>> while
>>>>>>>>>> "lig_new.pdb" is not running and is showing the sqm error. though
>>>> both
>>>>>>>> the
>>>>>>>>>> ligands are same and I am surprised why this error is coming.
>>>>>>>>>>
>>>>>>>>>> please help me as I am not able to troubleshoot.
>>>>>>>>>>
>>>>>>>>>> thank you
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
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>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
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>>>>>>>> AMBER mailing list
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>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>>
>>>>>>> *Mitul SrivastavaSenior Research FellowD*rug *D*iscovery *R*esearch
>>>>>> *C*enter
>>>>>>> (DDRC)
>>>>>>> *T*ranslational *H*ealth *S*cience and *T*echnology *I*nstitute
>>>> (THSTI),
>>>>>>> NCR Biotech Science Cluster
>>>>>>> 3rd Milestone, Faridabad – Gurgaon Expressway
>>>>>>> PO box #04, Faridabad – 121001, India
>>>>>>> <comp_usp7_s0.pdb><comp_lowest.pdb>___________________
>>>>>> ____________________________
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Received on Wed Feb 22 2017 - 01:00:05 PST
